Lia Thomas will be wiped from the University of Pennsylvania record books ... with the school agreeing to remove any trace of the transgender swimmer's success as part of a deal with the government.

The Department of Education announced the development on Tuesday ... saying the university entered into a resolution agreement to comply with Title IX after an investigation determined it broke the law by "allowing a male to compete in female athletic programs and occupy female-only intimate facilities."

As part of the agreement, UPenn will adhere to President Trump's "Keeping Men Out of Women's Sports" and "Defending Women from Gender Ideology Extremism" executive orders ... and will implement biology-based definitions for the words "male" and "female."

The school will also release a public statement on the matter ... and send a personalized apology to all impacted female swimmers who interacted with Thomas.

Thomas -- who won an NCAA championship in 2022 -- held the UPenn record in the 100-yard, 200-yard 500-yard freestyle events.

One of Thomas' opponents -- former University of Kentucky swimmer Riley Gaines -- released a statement on the matter ... saying, "From day one, President Trump and Secretary [Linda] McMahon vowed to protect women and girls, and today’s agreement with UPenn is a historic display of that promise being fulfilled."

"This Administration does not just pay lip service to women’s equality: it vigorously insists on that equality being upheld."